Variant report

Variant	rs11235109
Chromosome Location	chr11:87059742-87059743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10501636	0.89[ASN][1000 genomes]
rs10792942	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10792943	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10792944	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898662	0.90[AFR][1000 genomes]
rs10898667	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10898669	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10898673	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10898674	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10898675	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10898677	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898682	0.94[ASN][1000 genomes]
rs10898686	0.89[ASN][1000 genomes]
rs10898690	0.83[ASN][1000 genomes]
rs11235084	0.90[AFR][1000 genomes]
rs11235085	0.90[AFR][1000 genomes]
rs11235087	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11235088	0.92[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11235104	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11235105	0.95[ASN][1000 genomes]
rs11235106	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11235107	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11235110	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235122	0.97[ASN][1000 genomes]
rs11235130	0.94[ASN][1000 genomes]
rs11235137	0.83[ASN][1000 genomes]
rs11501862	0.94[ASN][1000 genomes]
rs11501863	0.94[ASN][1000 genomes]
rs11604458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12272915	0.90[AFR][1000 genomes]
rs12276145	0.92[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12279942	0.90[AFR][1000 genomes]
rs12281655	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12292705	0.81[MKK][hapmap]
rs12294015	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12295057	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12295490	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12361047	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12363349	0.96[CEU][hapmap];0.97[GIH][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12363623	0.94[ASN][1000 genomes]
rs12363892	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12790362	0.92[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2186727	0.80[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28395418	0.97[ASN][1000 genomes]
rs4245431	0.89[ASN][1000 genomes]
rs4453264	0.94[ASN][1000 genomes]
rs4471448	0.94[ASN][1000 genomes]
rs4536247	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4943983	0.89[ASN][1000 genomes]
rs4944698	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4944700	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944701	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7122267	0.94[ASN][1000 genomes]
rs7125169	0.94[ASN][1000 genomes]
rs7125381	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7938135	0.94[ASN][1000 genomes]
rs7951257	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1046288	chr11:86757573-87158571	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv555714	chr11:87058981-87399218	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11235109	C11orf73	cis	parietal	SCAN
rs11235109	PRSS23	cis	cerebellum	SCAN
rs11235109	CCDC89	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:87048400-87095400	Weak transcription	Aorta	Aorta
2	chr11:87055600-87063800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:87057400-87064000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:87058600-87063200	Weak transcription	Fetal Lung	lung
5	chr11:87058800-87059800	Enhancers	Fetal Intestine Large	intestine
6	chr11:87059000-87060400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr11:87059200-87063400	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:87059200-87064000	Weak transcription	Lung	lung
9	chr11:87059200-87065200	Weak transcription	Right Atrium	heart
10	chr11:87059600-87062800	Weak transcription	Fetal Stomach	stomach
11	chr11:87059600-87063800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:87059600-87064000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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